We are planning to port Biopython's documentation from the existing combination of LaTeX (cookbook and main docs) and EpyDoc (API docs) to [http://sphinx.pocoo.org/ Sphinx]. This is a multi-step process which we're proceeding through incrementally, and help is always appreciated. See the [https://redmine.open-bio.org/issues/3219 feature request].

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=== Extending Bio.PDB ===

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João Rodrigues's Summer of Code project aimed to introduce several new features to the Bio.PDB structural biology module: functions for adding polar hydrogens to structures, probing for SS bridges based on structural information and annotations, renumbering residues, coarse-graining a structure, etc. A more comprehensive layout of the project is available [[GSOC2010_Joao|on this wiki]], and the code is on [http://github.com/JoaoRodrigues/biopython/tree/GSOC2010 a GitHub branch]. New code for Bio.PDB was also written for [[Google_Summer_of_Code|GSoC 2011]]. João and Eric are now working to integrate this new code into Biopython.

=== Population Genetics development ===

=== Population Genetics development ===

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Brad is working on a Biopython GFF parser. Source code is available from [http://github.com/chapmanb/bcbb/tree/master/gff git hub]. Documentation is in progress at [[GFF Parsing]]. See blog posts on the [http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/ initial implementation] and [http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/ MapReduce parallel version].

Brad is working on a Biopython GFF parser. Source code is available from [http://github.com/chapmanb/bcbb/tree/master/gff git hub]. Documentation is in progress at [[GFF Parsing]]. See blog posts on the [http://bcbio.wordpress.com/2009/03/08/initial-gff-parser-for-biopython/ initial implementation] and [http://bcbio.wordpress.com/2009/03/22/mapreduce-implementation-of-gff-parsing-for-biopython/ MapReduce parallel version].

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=== Phylo ===

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[[User:EricTalevich|Eric]] is working on a new module for phylogenetics, [[Phylo|Bio.Phylo]]. It grew out of a [[Google Summer of Code]] 2009 [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798969 project], mentored by Brad, to add support for [http://www.phyloxml.org/ phyloXML] to Biopython; it also refactors part of Bio.Nexus. Most of the code has been pushed to the main development branch on GitHub already, but new features appear first on Eric's [http://github.com/etal/biopython/tree/phyloxml phyloxml branch].

=== Biogeography ===

=== Biogeography ===

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[[Matzke|Nick]] is working on developing a Biogeography module for BioPython. This work was funded by a [[Google Summer of Code]] 2009 [http://socghop.appspot.com/program/home/google/gsoc2009 project] through NESCENT's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors are [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd]. The code currently lives at the Bio/Geography directory of the [http://github.com/nmatzke/biopython/tree/Geography Geography fork of the nmatzke branch on GitHub], and you can see a timeline and other info about ongoing development [[BioGeography|here]]. The new module is being documented on this wiki as [[BioGeography]].

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Nick Matzke developed a biogeography module for BioPython as a [[Google Summer of Code]] project through NESCent's [https://www.nescent.org/wg_phyloinformatics/Phyloinformatics_Summer_of_Code_2009 Phyloinformatics Summer of Code 2009]. See the project proposal at: [http://socghop.appspot.com/student_project/show/google/gsoc2009/nescent/t124022798250 Biogeographical Phylogenetics for BioPython]. The mentors were [http://blackrim.org/ Stephen Smith] (primary), [http://bcbio.wordpress.com/ Brad Chapman], and [http://evoviz.nescent.org/ David Kidd]. The new module is documented on this wiki as [[BioGeography]].

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=== Roche 454 SFF parsing in Bio.SeqIO ===

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The code currently lives at the Bio/Geography directory of Nick's [http://github.com/nmatzke/biopython/tree/Geography Geography branch on GitHub], and Eric is preparing it for integration into the Biopython trunk on [http://github.com/etal/biopython/tree/geography another branch].

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See [http://bugzilla.open-bio.org/show_bug.cgi?id=2837 Bug 2837], based on code from Jose Blanca. Recently merged into the trunk and should be included in Biopython 1.54 onwards.

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=== RNA structure ===

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=== Multiple Sequence Alignments ===

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Several branches for working with RNA data have been made available by Kristian Rother. They can be used mainly for parsing RNA secondary structures [http://github.com/krother/biopython/tree/rna] and working with Bio.Sequence objects that represent modified RNA nucleotides [http://github.com/krother/biopython/tree/rna_alphabet].

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Peter is working on a new alignment class for sequence alignments (not the kind in next gen sequencing), the core of which was recently merged into the trunk and should be included in Biopython 1.54 onwards.

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=== Open Enhancement Bugs ===

=== Open Enhancement Bugs ===

This [http://bugzilla.open-bio.org/buglist.cgi?product=Biopython&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED&bug_severity=enhancement Bugzilla Search] will list all open enhancement bugs (any filed by core developers are fairly likely to be integrated, some are just wish list entries).

This [http://bugzilla.open-bio.org/buglist.cgi?product=Biopython&bug_status=NEW&bug_status=ASSIGNED&bug_status=REOPENED&bug_severity=enhancement Bugzilla Search] will list all open enhancement bugs (any filed by core developers are fairly likely to be integrated, some are just wish list entries).

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=== Branches on github.com ===

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The [http://github.com/biopython/biopython/network Biopython network diagram at github.com] will show all public branches of our repository on github, and will therefore let you see things that are being worked on.

== Project ideas ==

== Project ideas ==

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== Enhancement list ==

== Enhancement list ==

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Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our [http://bugzilla.open-bio.org/ bugzilla] page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.

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Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our [http://redmine.open-bio.org/projects/biopython Issue Tracker] page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.

Revision as of 17:53, 21 March 2013

This page provides a central location to collect references to active projects. This is a good place to start if you are interested in contributing to Biopython and want to find larger projects in progress. For developers, use this to reference git branches or other projects which you will be working on for an extended period of time. Please keep it up to date as projects are finished and integrated into Biopython.

Current projects

Porting Biopython documentation to Sphinx

We are planning to port Biopython's documentation from the existing combination of LaTeX (cookbook and main docs) and EpyDoc (API docs) to Sphinx. This is a multi-step process which we're proceeding through incrementally, and help is always appreciated. See the feature request.

Extending Bio.PDB

João Rodrigues's Summer of Code project aimed to introduce several new features to the Bio.PDB structural biology module: functions for adding polar hydrogens to structures, probing for SS bridges based on structural information and annotations, renumbering residues, coarse-graining a structure, etc. A more comprehensive layout of the project is available on this wiki, and the code is on a GitHub branch. New code for Bio.PDB was also written for GSoC 2011. João and Eric are now working to integrate this new code into Biopython.

Population Genetics development

Giovanni and Tiago are working on expanding population genetics code in Biopython. See the PopGen development page for more details.

RNA structure

Several branches for working with RNA data have been made available by Kristian Rother. They can be used mainly for parsing RNA secondary structures [1] and working with Bio.Sequence objects that represent modified RNA nucleotides [2].

Open Enhancement Bugs

This Bugzilla Search will list all open enhancement bugs (any filed by core developers are fairly likely to be integrated, some are just wish list entries).

Use SQLAlchemy, an object relational mapper, for BioSQL internals. This would add an additional external dependency to Biopython, but provides ready support for additional databases like SQLite. It also would provide a raw object interface to BioSQL databases when the SeqRecord-like interface is not sufficient. Brad and Kyle have some initial code for this.

Enhancement list

Maintaining software involves incremental improvements for new format changes and removal of bugs. Please see our Issue Tracker page for a current list. Post to the developer mailing list if you are interested in tackling any open issues.